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Nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

ABSTRACT:

Motivation

Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms.

Availability and implementation

The pipeline is freely available online on the nf-core website (https://nf-co.re/isoseq) and on GitHub (https://github.com/nf-core/isoseq) under MIT License (DOI: 10.5281/zenodo.7116979).

SUBMITTER: Guizard S

PROVIDER: S-EPMC10199315 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

Guizard Sébastien S Miedzinska Katarzyna K Smith Jacqueline J Smith Jonathan J Kuo Richard I RI Davey Megan M Archibald Alan A Watson Mick M

Bioinformatics (Oxford, England) 20230501 5

<h4>Motivation</h4>Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms.<h4>Ava ...[more]

PMID: 36961337

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